The leading cause of death in HIV-infected individuals.
Weakened immune system
Limits sensitivity of diagnosis of TB
Support vector machine to find 251-gene signature
Genes involved in Immunological, Infectious and Inflammatory Disease
Limits sensitivity of diagnosis of TB
Our aim:
Explore genes with a significant expression enriched in HIV with TB co-infection
Compare with the 251-gene signature found with the SVM model
Keep it clean and tidy:
Select variables
Mutate variables
Handle key-variable
Handle replications

Normalization - minimize technical variability
Log transformation - stabilize variance, reduce skewness
Quantile Normalization:
Variance explained by the principal components
First PC explains 15% of the variance
31 PCs needed to explain 90% of variance
Difficult to compress 47.000 onto few PCs
Scatter plot of projected observations onto PC1 and PC2
Slight division of disease state on PC1
No clear division of gender
Need for further analysis of disease state
Forest plot
Volcano plot